Center for Nonlinear Studies

Cooperative Phenomena in Soft Matter (2005-2007)

Soft matter systems have remarkable and complex properties ranging from the segregation of shaken granular matter and the jamming of colloids to the folding of proteins and the biological function of vesicles and membranes. We used tools of statistical mechanics, kinetic theory, non-equilibrium transport, classical elasticity theory, and quantum dynamics to explore collective phenomena of soft matter. Applications in real world materials include granular kinetics and dense granular flows, the statistical hydrodynamics of fluid turbulence, geometric and topological constraints in vesicles and membranes, polyelectrolyte assemblies, soft-hard interfaces, structure-geometry-function relationships in macromolecules, ultrafast spectroscopy in self-assembled structures, localization in bio-molecules, single molecule dynamics and the behavior of molecular machines. This work has programmatic applications in many areas of materials science including in applications of polymer coatings, high explosives packing, chem-bio threat reduction, and hard- soft interface electronics. An interdisciplinary approach combines experiment, numerics and theory across boundaries of physics, chemistry, biology and mathematics. There was particular emphasis in the following areas:

Energy landscapes in macromolecules
Colloids, vesicles, membranes
Dynamics of granular materials
Statistical hydrodynamics

Highlight Publications:

Chen, S., R. Ecke, G. Eyink, M. Rivera, M. Wan, and Z. Xiao. Physical mechanism of the two-dimensional inverse energy cascade. 2006. Physical Review Letters. 96 (8): 084502.
Chen, S.Y., G. L. Eyink, M. P. Wan, and Z. L. Xiao. Is the Kelvin theorem valid for high Reynolds number turbulence? 2006. Physical Review Letters. 97 (14): 144505.
Choi, C.H., A. Usheva, G. Kalosakas, K. O. Rasmussen, and A. R. Bishop. Comment on "Can one predict DNA transcription start sites by studying bubbles?". 2006. Physical Review Letters. 96 (23): 239801.
Connaughton, C., R. Rajesh, and O. Zaboronski. Constant flux relation for driven dissipative systems. 2007. Physical Review Letters. 98 (8): 080601.
Fraunfelder, H., P. Fenimore, G. Chen, and B. McMahon. Proteins: Slaving, folding and solvent effects. 2006. Proceedings of the National Academy of Sciences. 103 (42): 15469.
Hlavacek, W.S., J. R. Faeder, M. L. Blinov, R. G. Posner, M. Hucka, and W. Fontana. Rules for modeling signal-transduction systems. 2006. Sci STKE. 2006 (344): re6.
Libal, A., C. Reichhardt, and C. J. Reichhardt. Realizing colloidal artificial ice on arrays of optical traps. 2006. Physical Review Letters. 97 (22): 228302.
Libal, A., C. Reichhardt, B. Janko, and C. J. Reichhardt. Dynamics, rectification, and fractionation for colloids on flashing substrates. 2006. Physical Review Letters 96 (18): 188301.
Rapti, Z., A. Smerzi, K. O. Rasmussen, A. R. Bishop, C. H. Choi, and A. Usheva. Lengthscales and cooperativity in DNA bubble formation. 2006. Europhysics Letters. 74 (3): 540.
Sinitsyn, N.A., and I. Nemenman. The Berry phase and the pump flux in stochastic chemical kinetics. 2007. Europhysics Letters. 77 (5): 58001.
Turitsyn, K., M. Chertkov, V. Y. Chernyak, and A. Puliafito. Statistics of entropy production in linearized stochastic systems. 2007. Physical Review Letters. 98 (18): 180603.
Voulgarakis, N.K., A. Redondo, A. R. Bishop, and K. O. Rasmussen. Sequencing DNA by dynamic force spectroscopy: Limitations and prospects. 2006. Nano Letters. 6 (7): 1483.
Voulgarakis, N.K., A. Redondo, A. R. Bishop, and K. O. Rasmussen. Probing the mechanical unzipping of DNA. 2006. Physical Review Letters. 96 (24): 248101.
Weronski, P. Application of the extended RSA models in studies of particle deposition at partially covered surfaces. 2005. Advances in Colloid and Interface Science. 118 (1-3): 1.